05 June 2010

No one should take advice from this character, I'll grant you. But even King Richard II could see the obvious:

Then call them to our presence: face to face,
And frowning brow to brow, ourselves will hear
The accuser and the accused freely speak:
High-stomach’d are they both, and full of ire,
In rage deaf as the sea, hasty as fire.

So Richard Sternberg, that aggrieved martyr of the Smithsonian Institution, butchered at the hands of Evil Darwinists and now among his people in Seattle, has posted a nasty rebuttal to a three-month-old post of mine on Signature in the Cell. I had resolved to ignore the minions of that awful place, but I'll grace Richard with a response since he's found a mistake that I do need to correct.

The subject is "junk DNA," and I've written quite a lot about it. Poor Richard is mighty upset at one particular thing I wrote about the Captain of the Ship, Steve Meyer. Meyer trotted out the "junk DNA" pony, and started with the same tired baloney about how introns were "once thought to be nonfunctional 'junk DNA'" but are now "known to play many important functional roles in the cell." Richard doesn't like the fact that I refer to these claims as "ludicrous" and that I attribute the use of the "junk DNA" ploy to "some combination of ignorance, sloth, and duplicity."

Now before I address the scientific claims that Richard makes in his post (and in the disastrously clueless followup the same day), let me clarify my criticism of Meyer in my original post, because I think Sternberg is right to be annoyed by it.

My objection to Meyer's references to introns and "junk DNA" is more than just a quibble about the molecular biology of introns. I've explained before why I find the whole "junk DNA" mantra to be utterly duplicitous, and I referenced my previous writing in the critique of Meyer. The basic story told by DI propagandists and other creationists is that non-coding DNA was ignored for decades, during which it was thought to be completely functionless (due to "Darwinist" ideas), only to be dramatically revealed as centrally important to life. That story is false. The real story is more interesting and complex (of course) and has been explained in detail several times. (I and two other scientists were thinking of writing a review article on the subject, and I think we should revive that project.)

And so my response to Meyer's introduction of those silly ideas was very harshly dismissive. And, well, the problem is that Meyer's actual claim at that point in the book was fairly modest. The ploy is still duplicitous, and Meyer does in fact make ludicrous errors later in the book when discussing genomes, but Richard is all over me for blasting Meyer's little claim that introns "play many important functional roles in the cell." And I think he has a point. So first off:

Steve, I'm sorry for suggesting that you are duplicitous for pointing out that some introns play functional roles. Some do harbor functional elements, and perhaps many do, and while much certainly depends on what we all mean when we assign "functional roles" to large chunks of non-coding DNA, it's only fair to acknowledge that your statement is not strictly false.

But poor Richard. In his fiery haste to defend the Captain, and in his evident ignorance of the subject at hand, he botched his response, both by mangling the basic facts and by making a gratuitous assumption about what it means for an intron to have "function." And he projects a bizarre and extreme conception of intron "function" onto me, in a way that reveals a lot more about his thinking than it does about mine.

Here are my main comments on Richard's rebuttal.

1. Sternberg argues that because alternative splicing is biologically important, and because alternative splicing depends on the presence of splice junctions that are bounded by introns, then the facilitation of alternative splicing is a "function" of introns. I find that conclusion very odd. He's right that alternative splicing is an important and regulated process, and that intron sequences are involved in that process, and if that's all it takes for an intron (which can be far bigger than the splice junctions themselves) to be called "functional," then there are a lot of "functional" introns in the human genome.

But of course that's not what I and others mean when we question whether introns typically have "function." Since Larry Moran and I clearly know a whole lot more about molecular genetics than Richard does, you can assume that we both knew plenty about alternative splicing before we challenged the "introns have function" slogan. And that means that when we assert that introns don't tend to have "functions," we mean that the huge amounts of sequence within the introns don't tend to have "functions." I thought that was pretty obvious (I referred to it specifically in the original post), but Richard didn't, and I'm nice enough to assume that he just misunderstood. I'll even take the blame.

Sadly for Richard, his rebuttal and the response to Larry Moran showed that he doesn't understand RNA splicing, and in fact he appears not to understand the important and very basic distinction between a transcript and an intron. Read the comments at Sandwalk (Larry Moran's blog) to see why. I won't repeat it here, except to note that I was completely surprised by Sternberg's ignorance. It seems to me that he should spend a little more time actually trying to understand the science, and a little less time with the drill team.

2. Sternberg goes on to list various genomic elements – with various functions that have been established to varying degrees – that can be found in introns. His conclusion can be paraphrased like this:

DNA elements called yadas are sometimes found in introns. Yadas are thought to function in the control of stuff. Therefore introns control stuff.

And here's what this sounds like to me:

Paint cans are sometimes found in piles of rubbish in vacant urban lots (VULs). Paint cans can be used to prop up old cars, or to fight off intruders, or to make music. Therefore VULs are useful in auto repair, home security, and musical composition.

I hope you see that Sternberg's assertion, which is widely made by ID apologists and various creationists, is not so much wrong as it is just silly. And I hope it's a little clearer what I mean when I say that introns aren't known to be functional. Sternberg was wrong to assume that I would share his view of what it means for something to have "function," and he was doubly wrong to think that I would predict that introns don't sometimes – even often – contain elements that serve functional roles. Junkyards, after all, contain lots of stuff that can serve a function. (My previous attempt to illustrate this concept employed Yugos. Check it out. Todd Wood liked it too.)

3. Richard wonders why I didn't raise my intron question at the Q&A session at Biola. Since he was there, he knows that our time was quite short and that Steve Meyer did a lot of talking. He also knows that I did ask about DNA content in genomes, specifically, in my final question. Since Richard is so interested in such matters, I will be most eager to see his discussion of the information content of various animal genomes. Let me see if I can get things started.

Consider the green pufferfish. It's a pretty interesting creature: it puffs itself up to intimidate predators. More ominously, it sports a fearsome venom called tetrodotoxin that is much beloved of neuroscientists for its ability to block sodium channels (and thus nerve conduction). And consider the marbled lungfish. It has some notably peculiar traits, most obviously the ability to breathe air.

Just a couple of fish. The genome of the green pufferfish contains about 340 million bases. That's a lot of bases, but the pufferfish genome is about a tenth the size of the human genome. The genome of the marbled lungfish contains about 130 billion bases. That's about 40 times the size of the human genome. That means that the lungfish genome is almost 400 times the size of the pufferfish genome.

If you don't see why this is a huge problem for anyone who objects to the notion of non-functional DNA (and lots of it), then you should really lay off the Kool-Aid.

4. I mentioned in my last post that I would offer a personal response to Steve Meyer reflecting on our exchanges at Biola last month. I'll still do that. But I think it will be useful to send a clear message to the Discovery Institute as an organization, now that I've seen its mode of response to me since Meyer and I met. Here's my simple message:

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In rage deaf as the sea, hasty as fire.

No one should take advice from this character, I'll grant you. But even King Richard II could see the obvious:

Then call them to our presence: face to face,
And frowning brow to brow, ourselves will hear
The accuser and the accused freely speak:
High-stomach’d are they both, and full of ire,
In rage deaf as the sea, hasty as fire.

So Richard Sternberg, that aggrieved martyr of the Smithsonian Institution, butchered at the hands of Evil Darwinists and now among his people in Seattle, has posted a nasty rebuttal to a three-month-old post of mine on Signature in the Cell. I had resolved to ignore the minions of that awful place, but I'll grace Richard with a response since he's found a mistake that I do need to correct.

The subject is "junk DNA," and I've written quite a lot about it. Poor Richard is mighty upset at one particular thing I wrote about the Captain of the Ship, Steve Meyer. Meyer trotted out the "junk DNA" pony, and started with the same tired baloney about how introns were "once thought to be nonfunctional 'junk DNA'" but are now "known to play many important functional roles in the cell." Richard doesn't like the fact that I refer to these claims as "ludicrous" and that I attribute the use of the "junk DNA" ploy to "some combination of ignorance, sloth, and duplicity."

Now before I address the scientific claims that Richard makes in his post (and in the disastrously clueless followup the same day), let me clarify my criticism of Meyer in my original post, because I think Sternberg is right to be annoyed by it.

My objection to Meyer's references to introns and "junk DNA" is more than just a quibble about the molecular biology of introns. I've explained before why I find the whole "junk DNA" mantra to be utterly duplicitous, and I referenced my previous writing in the critique of Meyer. The basic story told by DI propagandists and other creationists is that non-coding DNA was ignored for decades, during which it was thought to be completely functionless (due to "Darwinist" ideas), only to be dramatically revealed as centrally important to life. That story is false. The real story is more interesting and complex (of course) and has been explained in detail several times. (I and two other scientists were thinking of writing a review article on the subject, and I think we should revive that project.)

And so my response to Meyer's introduction of those silly ideas was very harshly dismissive. And, well, the problem is that Meyer's actual claim at that point in the book was fairly modest. The ploy is still duplicitous, and Meyer does in fact make ludicrous errors later in the book when discussing genomes, but Richard is all over me for blasting Meyer's little claim that introns "play many important functional roles in the cell." And I think he has a point. So first off:

Steve, I'm sorry for suggesting that you are duplicitous for pointing out that some introns play functional roles. Some do harbor functional elements, and perhaps many do, and while much certainly depends on what we all mean when we assign "functional roles" to large chunks of non-coding DNA, it's only fair to acknowledge that your statement is not strictly false.

But poor Richard. In his fiery haste to defend the Captain, and in his evident ignorance of the subject at hand, he botched his response, both by mangling the basic facts and by making a gratuitous assumption about what it means for an intron to have "function." And he projects a bizarre and extreme conception of intron "function" onto me, in a way that reveals a lot more about his thinking than it does about mine.

Here are my main comments on Richard's rebuttal.

1. Sternberg argues that because alternative splicing is biologically important, and because alternative splicing depends on the presence of splice junctions that are bounded by introns, then the facilitation of alternative splicing is a "function" of introns. I find that conclusion very odd. He's right that alternative splicing is an important and regulated process, and that intron sequences are involved in that process, and if that's all it takes for an intron (which can be far bigger than the splice junctions themselves) to be called "functional," then there are a lot of "functional" introns in the human genome.

But of course that's not what I and others mean when we question whether introns typically have "function." Since Larry Moran and I clearly know a whole lot more about molecular genetics than Richard does, you can assume that we both knew plenty about alternative splicing before we challenged the "introns have function" slogan. And that means that when we assert that introns don't tend to have "functions," we mean that the huge amounts of sequence within the introns don't tend to have "functions." I thought that was pretty obvious (I referred to it specifically in the original post), but Richard didn't, and I'm nice enough to assume that he just misunderstood. I'll even take the blame.

Sadly for Richard, his rebuttal and the response to Larry Moran showed that he doesn't understand RNA splicing, and in fact he appears not to understand the important and very basic distinction between a transcript and an intron. Read the comments at Sandwalk (Larry Moran's blog) to see why. I won't repeat it here, except to note that I was completely surprised by Sternberg's ignorance. It seems to me that he should spend a little more time actually trying to understand the science, and a little less time with the drill team.

2. Sternberg goes on to list various genomic elements – with various functions that have been established to varying degrees – that can be found in introns. His conclusion can be paraphrased like this:

DNA elements called yadas are sometimes found in introns. Yadas are thought to function in the control of stuff. Therefore introns control stuff.

And here's what this sounds like to me:

Paint cans are sometimes found in piles of rubbish in vacant urban lots (VULs). Paint cans can be used to prop up old cars, or to fight off intruders, or to make music. Therefore VULs are useful in auto repair, home security, and musical composition.

I hope you see that Sternberg's assertion, which is widely made by ID apologists and various creationists, is not so much wrong as it is just silly. And I hope it's a little clearer what I mean when I say that introns aren't known to be functional. Sternberg was wrong to assume that I would share his view of what it means for something to have "function," and he was doubly wrong to think that I would predict that introns don't sometimes – even often – contain elements that serve functional roles. Junkyards, after all, contain lots of stuff that can serve a function. (My previous attempt to illustrate this concept employed Yugos. Check it out. Todd Wood liked it too.)

3. Richard wonders why I didn't raise my intron question at the Q&A session at Biola. Since he was there, he knows that our time was quite short and that Steve Meyer did a lot of talking. He also knows that I did ask about DNA content in genomes, specifically, in my final question. Since Richard is so interested in such matters, I will be most eager to see his discussion of the information content of various animal genomes. Let me see if I can get things started.

Consider the green pufferfish. It's a pretty interesting creature: it puffs itself up to intimidate predators. More ominously, it sports a fearsome venom called tetrodotoxin that is much beloved of neuroscientists for its ability to block sodium channels (and thus nerve conduction). And consider the marbled lungfish. It has some notably peculiar traits, most obviously the ability to breathe air.

Just a couple of fish. The genome of the green pufferfish contains about 340 million bases. That's a lot of bases, but the pufferfish genome is about a tenth the size of the human genome. The genome of the marbled lungfish contains about 130 billion bases. That's about 40 times the size of the human genome. That means that the lungfish genome is almost 400 times the size of the pufferfish genome.

If you don't see why this is a huge problem for anyone who objects to the notion of non-functional DNA (and lots of it), then you should really lay off the Kool-Aid.

4. I mentioned in my last post that I would offer a personal response to Steve Meyer reflecting on our exchanges at Biola last month. I'll still do that. But I think it will be useful to send a clear message to the Discovery Institute as an organization, now that I've seen its mode of response to me since Meyer and I met. Here's my simple message: